1
|
Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2:1430-1440. [PMID: 34704047 PMCID: PMC8496063 DOI: 10.1039/d1cb00138h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA-ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations.
Collapse
Affiliation(s)
- Takeshi Tabuchi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna Okinawa 904-0495 Japan
| |
Collapse
|
2
|
Ogawa A, Tabuchi J, Doi Y, Takamatsu M. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract. Bioorg Med Chem Lett 2016; 26:3658-61. [PMID: 27289318 DOI: 10.1016/j.bmcl.2016.05.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity.
Collapse
Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Takamatsu
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
3
|
|
4
|
Xu Q, Zhang CY. Riboadenosine-substituted DNA probes for self-illuminating real-time monitoring of exonuclease III activity and exonuclease III-assisted target recycling. Chem Commun (Camb) 2014; 50:8047-9. [DOI: 10.1039/c4cc03021d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
5
|
Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | | | | | | | | |
Collapse
|
6
|
Xu Q, Cao A, Zhang LF, Zhang CY. Rapid and Label-Free Monitoring of Exonuclease III-Assisted Target Recycling Amplification. Anal Chem 2012; 84:10845-51. [DOI: 10.1021/ac303095z] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Qinfeng Xu
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Anping Cao
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ling-fei Zhang
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Weihai Municipal Center for Disease Control and Prevention, Shandong
264200, China
| | - Chun-yang Zhang
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
7
|
Ogawa A. Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands. Bioorg Med Chem Lett 2012; 22:1639-42. [DOI: 10.1016/j.bmcl.2011.12.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 12/26/2011] [Accepted: 12/26/2011] [Indexed: 11/16/2022]
|
8
|
Ogawa A. Multiple-Catalytic Sensing of Nucleic Acid Sequences by Utilising a DNA-RNA-DNA Chimeric Antisense Probe and RNase H with a Eukaryotic Cell-Free Translation System. Chembiochem 2011; 12:881-5. [DOI: 10.1002/cbic.201000744] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 02/05/2023]
|
9
|
Sando S. Design of Functional Nucleic Acid Systems for Biomolecular Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
10
|
The ODN probes conjugating the Cu(II) complex enhance the luminol chemiluminescence by assembling on the DNA template. Bioorg Med Chem 2010; 18:8614-7. [PMID: 21115284 DOI: 10.1016/j.bmc.2010.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/02/2010] [Accepted: 10/05/2010] [Indexed: 11/21/2022]
Abstract
Potent peroxidase-like activity of the β-ketoenamine (1)-dicopper (II) complex (2) for the chemiluminescence (CL) of luminol either in the presence or absence of H(2)O(2) has been previously demonstrated by our group. In this study, the β-ketoenamine (1) as the ligand unit for copper(II) was incorporated into the oligonucleotide (ODN) probes. It has been shown that the catalytic activity of the ODN probes conjugating the ligand-Cu(II) complex is activated by hybridization with the target DNA with the complementary sequence. Thus, this study has successfully demonstrated the basic concept for the sensitive detection of nucleic acids by CL based on the template-inductive activation of the catalytic unit for CL.
Collapse
|
11
|
Ogawa A. Isothermal sensitive detection of microRNA using an autonomous DNA machine recycling output as input. Bioorg Med Chem Lett 2010; 20:6056-60. [DOI: 10.1016/j.bmcl.2010.08.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 08/10/2010] [Accepted: 08/11/2010] [Indexed: 11/30/2022]
|
12
|
Aoyama Y. Structure and Function of Molecular Assembly. A Personal Reminiscence. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.419] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
13
|
Sando S, Narita A, Hayami M, Aoyama Y. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun (Camb) 2008:3858-60. [PMID: 18726014 DOI: 10.1039/b808449a] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "light-up" RNA aptamer-Hoechst pair can be used as a fluorescent tag to monitor transcription processes.
Collapse
Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.
| | | | | | | |
Collapse
|
14
|
Sando S, Narita A, Aoyama Y. Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. Chembiochem 2008; 8:1795-803. [PMID: 17806095 DOI: 10.1002/cbic.200700325] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have designed a strategy to generate a light-up fluorophore-aptamer pair based on a down-modification of a conventional DNA-staining dye to suppress its affinity to the original dsDNA targets, followed by reselection of aptamers that would bind to the modified dye. Following this line, we prepared a micropolarity-sensitive Hoechst derivative possessing two tBu groups with low affinity to the usual AT-rich dsDNA targets. DNA aptamers selected in vitro from a random pool worked as triggers to enhance the fluorescence of an otherwise nonfluorescent Hoechst derivative, and the shortened 25-mer sequence showed remarkable enhancement (light-up). The 25-mer sequence was split into binary aptamer probes, thus enabling us to detect a target nucleic acid sequence with a single-nucleotide resolution by use of unmodified DNA as a probe.
Collapse
Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | | | | |
Collapse
|
15
|
Narita A, Ogawa K, Sando S, Aoyama Y. Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution. Nat Protoc 2008; 2:1105-16. [PMID: 17546001 DOI: 10.1038/nprot.2007.140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA sensing at a single nucleotide resolution is achieved using a hairpin-shaped, unmodified (unlabeled) RNA probe or the precursor double-stranded DNA (dsDNA) in a prokaryotic cell-free translation medium. The molecular-beacon-like probe consists of a loop region that is complementary to the target sequence and a stem composed of a ribosome-binding site (RBS) and its docking domain; the RBS is followed by the gene for a reporter protein such as luciferase or beta-galactosidase. Target binding at the loop opens the hairpin to make RBS accessible by the ribosome to start translation of the reporter protein. This sensing system is signal amplifying by virtue of catalytic DNA-to-RNA transcription when using a dsDNA probe, catalytic RNA-to-protein translation, catalytic signal transduction by the enzymatic reaction of the translated reporter protein and, in the presence of RNase H, catalytic or even irreversible translation-activation of the target-probe heteroduplex. Preparation of a probe takes 1-3 d and gene sensing using the probe takes 1-3 h.
Collapse
Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | |
Collapse
|
16
|
Ogawa A, Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007; 17:3156-60. [PMID: 17391960 DOI: 10.1016/j.bmcl.2007.03.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/07/2007] [Accepted: 03/10/2007] [Indexed: 11/20/2022]
Abstract
We constructed a label-free and detector-free aptazyme-based riboswitch sensor for detecting the cofactor of the aptazyme. This riboswitch, which usually suppresses the gene expression with its anti-RBS sequence bound to the RBS of its own mRNA (OFF), activates the translation only when a cofactor is added to release the anti-RBS sequence from itself as a result of cofactor-induced self-cleavage by the aptazyme (ON). The rationally optimized one with beta-galactosidase as a reporter gene enabled us to detect the cofactor of the aptazyme visibly with high ON/OFF efficiency.
Collapse
Affiliation(s)
- Atsushi Ogawa
- Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | | |
Collapse
|